Knuckles is dozing off in front of the Master Emerald when it suddenly shatters and a liquid being emerges and knocks him away. The shards fly away, and he goes hunting for them. He heads to Station Square and finds some shards in Speed Highway. Then he heads to Casinopolis to find more. He heads into Station Square hotel and sees Eggman holding an emerald. He chases him up the elevator and ends up in a battle with Chaos 2.

He then heads to Mystic Ruin and goes emerald hunting in Red Mountain. He exits here and sees Sonic and Tails by the lake. He battles them, and they lose the emeralds to Eggman. Eggman gives them to Chaos, and they all battle Chaos 4.

Knuckles heads to the jungle where Tikal helps him to figure out how to open up the Echidna Temple. He then picks up shards in Lost World. He goes and puts the shards back on the emerald, but sees some are still missing. The Egg Carrier's image appears in the emerald, so Knuckles wastes no time. He finds the last shards in the Sky Deck, but before he can leave he has to have one last battle with Chaos 6. He the heads back to the Floating island and repairs the Emerald, and goes back to his guardian life.